palmid (version 0.0.3)

PlotOrgn: Plot a wordcloud of the organisms in a palm.sra object or orgn.vec

Description

Plot a wordcloud of the organisms in a palm.sra object or orgn.vec

Usage

PlotOrgn(palm.sra = NULL, orgn.vec = NULL, freq = T)

Arguments

palm.sra

data.frame, created from get.palmSra() [NULL]

orgn.vec

character, vector of "scientific_name" from sra run table [NULL]

freq

boolean, scale words by frequency, else by identity [T]

Value

A ggwordcloud object of the "ntop" frequent terms

Examples

# NOT RUN {
# Retrive organism identifiers from SRA Run Info Table
# palm.orgn <- get.sraOrgn(run_ids, con)

# Load Waxsystermes Exampel data
data("waxsys.palm.sra")

# Create wordcloud of organism terms
# using column "scientific_name" in data.frame

# Scaled by frequency of organism term in all of data.frame
PlotOrgn( waxsys.palm.sra )

# Scaled by proximity of organism tag to input sequence (pident)
PlotOrgn( waxsys.palm.sra , freq = FALSE)

# }